7VSD

E. coli Ribonuclease HI in complex with one Mg2+ (2)

7VSD の概要

• エントリーDOI: 10.2210/pdb7vsd/pdb
• 分子名称: Ribonuclease HI, SULFATE ION, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: endonuclease, metalloenzyme, hydrolase
• 由来する生物種: Escherichia coli (strain K12)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 35511.04

構造登録者

Liao, Z.,Oyama, T. (登録日: 2021-10-26, 公開日: 2022-03-02, 最終更新日: 2023-11-29)

主引用文献

Liao, Z.,Oyama, T.,Kitagawa, Y.,Katayanagi, K.,Morikawa, K.,Oda, M.
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.
Acta Crystallogr D Struct Biol, 78:390-398, 2022

PubMed Abstract: The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme-Mg complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme-Zn complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.

PubMed: 35234152
DOI: 10.1107/S2059798322000870

実験手法

X-RAY DIFFRACTION (1.7 Å)